Evaluate gene sets identified by SDAN
Wei Sun
2024-07-12
Setup
Check enrichment of gene sets
Read in gene info and gene set assignments
cell_type_name = "CD8T"
file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 24.0 25.0 26.0 25.8 27.0 28.0## [1] 40## [1] 24 24 24 24 25 25 25 25 25 25 25 25 25 25 25 25 25 26 26 26 26 26 26 26 26
## [26] 26 26 26 27 27 27 27 27 27 27 27 27 27 27 28## [1] 1032Find gene symbols
Find gene symbols from bioMart.
All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]Find gene symbols using the alias2Symbol function from
limma.
a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "C7orf55"
## [1] "FMC1-LUC7L2" "FMC1"
## [1] "MARS"
## [1] "MARS1" "SLA2"
## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "APITD1"
## [1] "CENPS-CORT" "CENPS"
## [1] "HIST1H2BC"
## [1] "H2BC5" "H2BC4"##
## FALSE TRUE
## 1120 139##
## FALSE TRUE <NA>
## 71 1049 139gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: ZNRD1 POLR1H
## 2: C2orf43 LDAH
## 3: FAM45A DENND10
## 4: MTERF MTERF1
## 5: NARG2 ICE2
## 6: C6orf203 MTRES1
## 7: HRSP12 RIDA
## 8: FOPNL CEP20
## 9: WARS WARS1
## 10: LINS LINS1
## 11: RRNAD1 METTL25B
## 12: FAM122B PABIR2
## 13: WDYHV1 NTAQ1
## 14: HIST1H2BD H2BC5
## 15: AGPAT6 GPAT4
## 16: C1orf123 CZIB
## 17: KIAA1841 SANBR
## 18: C2orf44 WDCP
## 19: TMEM155 SMIM43
## 20: C7orf55 FMC1-LUC7L2
## 21: C9orf89 CARD19
## 22: C11orf82 DDIAS
## 23: XRCC6BP1 ATP23
## 24: MARS MARS1
## 25: C19orf55 PROSER3
## 26: HIST1H2AE H2AC8
## 27: QARS EPRS1
## 28: APITD1 CENPS-CORT
## 29: CCDC101 SGF29
## 30: PDDC1 GATD1
## 31: EFCAB4A CRACR2B
## 32: EIF2S3L EIF2S3B
## 33: HIST1H2BC H2BC5
## 34: WRB GET1
## 35: TMEM194B NEMP2
## 36: HIST1H4C H4C3
## 37: HIST1H4J H4C11
## 38: ZNF720 KRBOX5
## 39: HIST1H2BH H2BC9
## 40: FAM49A CYRIA
## 41: TTC37 SKIC3
## 42: C1orf85 GLMP
## 43: C9orf114 SPOUT1
## 44: HIST2H2AA4 H2AC19
## 45: HIST2H2BF H2BC18
## 46: C10orf128 TMEM273
## 47: TCTEX1D2 DYNLT2B
## 48: C17orf89 NDUFAF8
## 49: PHBP3 PHB1P3
## 50: SEPT7P7 SEPTIN7P7
## 51: LINC00493 SMIM26
## 52: HIST1H2BN H2BC15
## 53: ATP5J2 ATP5MF
## 54: AKAP2 PALM2AKAP2
## 55: WDR65 CFAP57
## 56: SRP14-AS1 SRP14-DT
## 57: CTC-436P18.1 SMIM15-AS1
## 58: HIST1H3G H3C8
## 59: EFTUD1P1 EFL1P1
## 60: ATP5A1P3 ATP5F1AP3
## 61: CCDC109B MCUB
## 62: C1orf63 RSRP1
## 63: TMEM66 SARAF
## 64: PCNXL2 PCNX2
## 65: ACRC GCNA
## 66: AMICA1 JAML
## 67: PRMT10 PRMT9
## 68: FAM102A EEIG1
## 69: SELM SELENOM
## 70: NBPF16 NBPF15
## 71: RPL9P9 RPL9P8
## sym_in_data sym_limmagene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma), gene_symbol := sym_limma]
dim(gene_info)## [1] 1259 3## sym_in_data sym_limma gene_symbol
## 1: C1orf112 C1orf112 C1orf112
## 2: MAD1L1 MAD1L1 MAD1L1
## 3: ICA1 ICA1 ICA1
## 4: NDUFAF7 NDUFAF7 NDUFAF7
## 5: ST7 ST7 ST7## t1
## 1 2
## 1255 2## sym_in_data sym_limma gene_symbol
## 1: HIST1H2BD H2BC5 H2BC5
## 2: HIST1H2BC H2BC5 H2BC5
## 3: RPL9P8 RPL9P8 RPL9P8
## 4: RPL9P9 RPL9P8 RPL9P8Prepare gene set information
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
gmtfile[["immune"]] = "../Annotation/c7.all.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp" "immune"## reactome go_bp immune
## 1692 7647 5219Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
##
## $immune
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5 162 193 197 199 199 200 200 200 200 1992Conduct enrichment analysis
## [1] 1259 3## sym_in_data sym_limma gene_symbol
## 1: C1orf112 C1orf112 C1orf112
## 2: MAD1L1 MAD1L1 MAD1L1max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol")
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=120)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "MAP4K5" "PAFAH1B3" "SPTLC2" "CAPN15" "PIEZO1" "RASSF4"
## [7] "CACYBP" "CCR2" "NUP85" "UROD" "NPHP4" "HRSP12"
## [13] "ANXA1" "ASNSD1" "MZT2B" "CENPH" "RNF207" "C1orf123"
## [19] "RNF25" "LRRC28" "UBB" "HSPA1B" "MYCBP" "TMEM63A"
## [1] 2
## [1] "IL4R" "UTP6" "ACVR1" "SMUG1" "GLUL"
## [6] "GNG4" "ZNF816" "RPS27AP2" "CTB-33G10.1" "TXK"
## [11] "ARRDC2" "RASGRF2" "EGR1" "ACVR2A" "FOSB"
## [16] "JUND" "SKIL" "SORL1" "SGSM2" "GNAQ"
## [21] "LDLRAP1" "DHRS3" "TC2N" "TMEM150A" "DNHD1"
## [1] 3
## [1] "CCL3" "TIMM21" "WDR7" "THOC5" "PON2" "KLRB1"
## [7] "BRD8" "EMG1" "CCL4" "ACTR10" "KLRC1" "GCHFR"
## [13] "CXCL13" "PANK4" "C19orf47" "EXTL2" "GTSF1" "METTL18"
## [19] "WRB" "COA3" "CMC1" "CCL4L2" "MSH5" "CCL4L1"
## [25] "CCL3L1" "KLRC2"
## [1] 4
## [1] "ID3" "PARP2" "MMS22L" "PLIN2"
## [5] "ATF3" "HIST1H2BC" "PLA2G6" "HIST2H2AA4"
## [9] "HIST1H2BN" "HIST1H3G" "RP11-386G11.10" "IFRD1"
## [13] "RGCC" "NR4A3" "RASGEF1B" "NR4A2"
## [17] "TIPARP" "PRMT10" "PFKFB3" "RBKS"
## [21] "CHD2" "ANKRD37" "MTND1P23" "PSMD6-AS2"
## [25] "KCNQ1OT1" "RP11-434H6.7"
## [1] 5
## [1] "ZNF419" "FAM45A" "RNF121" "NDUFAF6"
## [5] "TMSB15B" "CCDC28B" "ZBTB39" "RHEBL1"
## [9] "LRRC45" "RP11-23P13.6" "ZNF93" "ENTPD5"
## [13] "ZNF511" "ZNF525" "RP11-122G18.7" "AC115617.2"
## [17] "RP11-262H14.3" "AC007041.2" "AC004069.2" "MIR146A"
## [21] "RPPH1" "PMF1-BGLAP" "RP11-209D14.4" "AL358333.1"
## [25] "CTD-3214H19.4" "CTD-2545M3.2" "RP11-282O18.6"
## [1] 6
## [1] "NT5C2" "PMM1" "GALK1" "GNPTAB"
## [5] "STYXL1" "PGPEP1" "XAF1" "AHI1"
## [9] "CLSTN3" "WARS" "TATDN1" "TMPRSS3"
## [13] "DNAJC18" "TMEM107" "SPATA13" "PSMG1"
## [17] "TNFRSF18" "EFCAB7" "TRGV3" "RP11-64B16.2"
## [21] "RP11-247I13.3" "RP5-1053E7.3" "UBXN2B" "RP11-782C8.1"
## [25] "PSMC1P9" "EFTUD1P1"
## [1] 7
## [1] "MCM9" "TMEM241" "KHDC1" "IRF8"
## [5] "MPPE1" "SLAMF8" "FCRL3" "MGAT4B"
## [9] "AMDHD2" "LZTFL1" "PRIMPOL" "GNGT2"
## [13] "TRIM68" "NINJ2" "ZBTB8OS" "ABHD16B"
## [17] "PTGES3P2" "PHBP3" "GS1-124K5.2" "PA2G4P4"
## [21] "NPM1P34" "BDH2P1" "RP11-552M11.4" "MS4A1"
## [25] "SERHL2"
## [1] 8
## [1] "TRPT1" "TRBV4-2" "TRAV12-2" "RP11-383G10.3"
## [5] "RPS19P1" "NPM1P19" "Z97634.3" "RP11-32B5.1"
## [9] "NDUFA9P1" "RP11-33B1.1" "HNRNPA1P50" "DGKA"
## [13] "TCF7" "CCR7" "PCNXL2" "CDC42EP3"
## [17] "ZBTB20" "DENND5A" "POU6F1" "SELL"
## [21] "RPS26P6" "RP11-91K8.4" "WHAMMP2" "TMEM9B-AS1"
## [25] "RP11-747H7.3" "CTD-2017D11.1" "RP11-51J9.5"
## [1] 9
## [1] "APH1B" "SEC24D" "ATF4P3" "RPL7AP31"
## [5] "HNRNPA1P55" "HNRNPA1P16" "APBA2" "TMEM66"
## [9] "ZMAT1" "NPIPB3" "AC018720.10" "EIF1"
## [13] "NR1D2" "NPIPB4" "HLA-J" "RP11-572P18.1"
## [17] "MTND2P28" "CTD-2328D6.1" "RPL41" "ACTBP12"
## [21] "RPS3AP6" "HLA-W" "NPIPB5" "MTATP6P1"
## [25] "RP11-320M16.1" "CTD-2031P19.4"
## [1] 10
## [1] "SMG6" "DUSP12" "MICALL1" "CNOT2" "RCOR3" "MTFR1L"
## [7] "CCDC77" "METTL8" "FOPNL" "CASP1" "KSR1" "VPS37A"
## [13] "TMEM208" "TMEM126A" "CEP63" "CNOT10" "CEP57L1" "RN7SL749P"
## [19] "TNRC6C" "CLDND1" "TNRC6B" "CNOT6L" "BTG2" "RALGAPA1"
## [25] "PLA2G4B"
## [1] 11
## [1] "POLA2" "USP28" "WDR3" "WIPI1" "PIK3C3"
## [6] "ULK2" "WDR13" "IFIT3" "IFIT2" "L3HYPDH"
## [11] "RSAD2" "BCAS3" "PELP1" "BAP1" "WDR41"
## [16] "PHAX" "ATG13" "IFIT1" "PIK3R4" "MBD5"
## [21] "CATSPER2P1" "RAB12" "C9orf72" "FBXO32"
## [1] 12
## [1] "CD200" "OCEL1" "MS4A6A" "PDE6B"
## [5] "NUDT7" "TMEM138" "TMEM155" "C9orf89"
## [9] "GSTM4" "NME6" "EEF1GP1" "TMEM194B"
## [13] "RSC1A1" "AC009403.2" "RP3-340B19.5" "PGAM4"
## [17] "RP11-247I13.6" "AC090804.1" "BHLHE40-AS1" "GAPDHP2"
## [21] "FAM21FP" "KB-1507C5.2" "SF3A3P2" "AP000620.1"
## [25] "MTRNR2L3" "RP11-493L12.6" "AC006129.4"
## [1] 13
## [1] "TM7SF3" "MAP3K13" "POLD3" "AAAS"
## [5] "TIMM9" "PLA2G15" "POP4" "FAHD2A"
## [9] "GALE" "NR2C1" "TIMM10" "FHOD1"
## [13] "UCK2" "GALK2" "XRCC6BP1" "MEI1"
## [17] "POP5" "CTDNEP1" "DALRD3" "PIGW"
## [21] "WDR53" "UCKL1" "ABHD14A" "RP11-304L19.5"
## [25] "GGT7" "OBSCN"
## [1] 14
## [1] "CRTAM" "TFDP2" "IRF4" "KIR3DL1"
## [5] "TMEM134" "AC004840.9" "SMIM19" "FCRL6"
## [9] "SLC9A9" "FAM49A" "ZNF649" "NPM1P32"
## [13] "CD27-AS1" "RNU2-63P" "RP11-567G24.1" "PATL2"
## [17] "SEPT7P7" "GYG1P3" "BTF3P10" "ERP29P1"
## [21] "RP11-254B13.4" "AC011747.4" "STARD4-AS1" "GAPDHP38"
## [25] "RNU1-125P" "AL161784.1" "AOAH"
## [1] 15
## [1] "EVC" "LTBP4" "ARHGEF18" "SCRN2"
## [5] "GPN2" "OXSM" "FAM122B" "DBF4B"
## [9] "TAF10" "CCDC101" "ZBED2" "RP11-773D16.1"
## [13] "RP11-119F19.2" "AC093391.2" "MAK" "MAN1C1"
## [17] "ATXN7" "POLR2J3" "YPEL2" "TTC3"
## [21] "PLGLB1" "NELL2" "MIR4461" "GPRASP1"
## [25] "RP11-514P8.6" "LINC00944"
## [1] 16
## [1] "STAU2" "NOP16" "YBX3" "NTHL1" "SART3" "KHSRP"
## [7] "FMR1" "DOT1L" "DHX58" "DKC1" "APTX" "UTP23"
## [13] "HIST1H2BD" "MARS" "KBTBD2" "PCGF5" "ZFP62" "ZNF770"
## [19] "C9orf114" "ZBTB48" "MIR29B1" "PDCD4" "ZNF589" "TSPYL2"
## [1] 17
## [1] "C1orf112" "VPS41" "AGA" "BCL3" "RNF13" "CDKL1"
## [7] "GSR" "TYK2" "SNX8" "NCOA7" "FIGNL1" "TTLL4"
## [13] "IDH1" "TMOD3" "TAMM41" "WDR43" "COG5" "ETFDH"
## [19] "ZNF431" "ANKRD28" "TREX1" "IFRD2" "PPIL3" "PLXND1"
## [25] "SELM"
## [1] 18
## [1] "MAD1L1" "RNF10" "PTPN18" "GABPB1" "SMC4" "C3orf14"
## [7] "STK25" "CKS2" "CCNB1" "PMAIP1" "HIRIP3" "CCNB2"
## [13] "ANAPC10" "CTSB" "TBCA" "RRM2" "ASB8" "EDARADD"
## [19] "TDRD7" "HIST1H4C" "DDX3Y" "FAM117B" "NPAT" "PLK3"
## [25] "TSC22D2"
## [1] 19
## [1] "DYRK4" "ZNF684" "C2orf43" "DTD2"
## [5] "SLC35A5" "ZNF80" "ZNF678" "ZNF749"
## [9] "C10orf128" "TRAV16" "AC018804.7" "XXbac-B562F10.11"
## [13] "KIR2DS4" "AC012318.3" "GK3P" "GOT2P3"
## [17] "LINC00484" "AC002331.1" "RP11-305L7.3" "CTD-2301A4.3"
## [21] "AC005329.7" "RP11-473N11.2" "AP000462.1" "RP11-317N8.4"
## [25] "CD248" "CHRM3-AS2" "RP1-187B23.1" "RP11-1000B6.3"
## [1] 20
## [1] "RP3-324O17.4" "NSMCE4A" "NAP1L4P1" "MTHFD2P7"
## [5] "CCDC30" "TRBV20-1" "RP11-365H23.1" "AC009506.2"
## [9] "CNOT7P1" "ETF1P2" "RPL37P23" "HSPA8P4"
## [13] "CTC-436P18.1" "TRAV1-2" "RP11-511H9.4" "ANP32AP1"
## [17] "HMGB1P8" "RCAN3" "NEK1" "ACRC"
## [21] "FILIP1L" "TCEAL3" "AC084018.1" "LINC00674"
## [25] "RP11-44N11.1" "RP11-727F15.9" "QRSL1P3"
## [1] 21
## [1] "TBPL1" "DUS4L" "LOXL3" "FANCL"
## [5] "CD160" "DHDDS" "NPC2" "MCEE"
## [9] "MT2A" "MTHFS" "GTF2A2" "USF1"
## [13] "KIAA1841" "NFU1" "MT1E" "MT1X"
## [17] "TECPR1" "TRAV13-1" "TSTD1" "RNU2-2P"
## [21] "UBE2D3P2" "PET100" "LINC00493" "RP11-1012A1.7"
## [25] "MIR142"
## [1] 22
## [1] "GBA2" "DERL2" "ERGIC2" "RABGGTA" "ILVBL" "GOSR2"
## [7] "CPD" "SRM" "NQO2" "PPFIA1" "FADS2" "MAP3K6"
## [13] "LIMD1" "FADS1" "AMFR" "FRS2" "JSRP1" "PAAF1"
## [19] "NT5DC1" "CSNK1A1L" "AGER" "DKK3" "EPHA4" "MPP7"
## [25] "KLHL25"
## [1] 23
## [1] "ZNF268" "FAH" "ZNF85" "PECR"
## [5] "CCRL2" "MTERF" "RRNAD1" "ADCK5"
## [9] "SNHG11" "GEN1" "C2orf76" "ZNF257"
## [13] "ANAPC10P1" "RP4-694B14.5" "PIN4P1" "RP3-342P20.2"
## [17] "ZNF826P" "RPL13P5" "RN7SL56P" "TPM3P6"
## [21] "RNF138P1" "RP11-889L3.4" "RP11-844P9.3" "RP11-638I2.10"
## [25] "CTD-2022H16.3" "CTB-31O20.3" "RP11-297D21.4"
## [1] 24
## [1] "DEPDC5" "PIM2" "FGFBP2" "PPCDC"
## [5] "DEF8" "PPOX" "SPON2" "FCGR3B"
## [9] "CX3CR1" "ITGAM" "EIF2S3L" "FCGR3A"
## [13] "HIST2H2BF" "TRAV35" "RP11-270C12.3" "RPS12P26"
## [17] "SNRPEP4" "PTGES3P1" "FAM200B" "RP11-81H14.2"
## [21] "MIR3615" "LUZP6" "AC024592.12" "FRMD4A"
## [25] "PER1"
## [1] 25
## [1] "MFAP3" "TNFRSF9" "C14orf93" "SLC25A14" "SLC11A2"
## [6] "MDGA1" "CD86" "TNFSF10" "IFI6" "DPH6"
## [11] "IFI44L" "IFI44" "LAIR2" "TRANK1" "CXCR6"
## [16] "TRBV9" "TRAV19" "CRYGS" "AC104820.2" "MIR155HG"
## [21] "AC092580.4" "AKAP2" "CCL3L3" "RP11-345J4.6" "AMICA1"
## [26] "MUC20"
## [1] 26
## [1] "DHPS" "DHRS12" "ENO3" "PRR4" "PTP4A1"
## [6] "MYB" "CLU" "NARF" "MTF2" "SUV39H2"
## [11] "SFR1" "NAA15" "FBXO22" "SWI5" "RMDN1"
## [16] "BOLA1" "KATNA1" "DUSP28" "ZNF544" "WDHD1"
## [21] "RP13-638C3.4" "PMEPA1" "LEF1" "NAA16" "GOLGA8A"
## [1] 27
## [1] "REXO1" "ZNF683" "PDCL3P5" "AC098614.2"
## [5] "NPM1P33" "CALM2P3" "TCP1P1" "AC144530.1"
## [9] "CDC42P1" "RP3-395M20.8" "RP11-382J24.2" "HSPA8P5"
## [13] "AC006483.1" "AC139149.1" "MIR3661" "RASGRP2"
## [17] "CPQ" "FOXP1" "C1orf162" "PLAC8"
## [21] "FAM102A" "GPR183" "SATB1" "CTD-3092A11.1"
## [25] "RP11-632K20.7" "RP1-313I6.12"
## [1] 28
## [1] "CHI3L2" "PUS7L" "IL10" "XCL1"
## [5] "XCL2" "CMAHP" "ZNF720" "RPSAP54"
## [9] "LDHBP2" "MYL5" "RP11-2F9.3" "ARPC3P1"
## [13] "HNRNPKP2" "RPL19P21" "SKP1P1" "RPS11P5"
## [17] "EEF1A1P14" "RAB1C" "AP000476.1" "RPS19P3"
## [21] "AC018462.3" "EEF1A1P10" "RP11-179A18.1" "SRP14-AS1"
## [25] "RP11-686D22.10" "RP4-739H11.4" "AP001468.1"
## [1] 29
## [1] "GZMB" "GMPR2" "NHP2P1" "IL18RAP"
## [5] "PTGER2" "NARG2" "FUOM" "TNFAIP8L2"
## [9] "HOPX" "ARHGAP11B" "TRAV14DV4" "TRAV29DV5"
## [13] "RP13-383K5.4" "KANSL1-AS1" "RP4-742C19.12" "RP11-350G13.1"
## [17] "RP4-800M22.1" "PRDX3P1" "TPI1P2" "ADH5P4"
## [21] "RP11-446E9.1" "GAPDHP60" "RP11-402J6.3" "USP30-AS1"
## [25] "SNORD3A" "TPMTP1" "CTB-52I2.4"
## [1] 30
## [1] "EVI5" "CDKN3" "RAD51C" "STMN1"
## [5] "TXNDC17" "TROAP" "BORA" "GEMIN6"
## [9] "MITD1" "PAQR4" "CDCA7L" "C11orf82"
## [13] "ZFYVE19" "UBE2C" "TYMS" "LRTOMT"
## [17] "SESTD1" "TCTEX1D2" "NCKIPSD" "MDP1"
## [21] "RP11-378G13.2" "SAPCD1" "PAICSP4" "HMGB1P24"
## [25] "RP11-307P22.1" "RP11-265N6.2"
## [1] 31
## [1] "P2RX5" "PRMT7" "SNX14" "PWP1" "ACTL6A" "PRSS23"
## [7] "CXXC1" "TOMM40L" "B2M" "CAPN12" "AFMID" "KNTC1"
## [13] "TMEM120A" "TMSB4X" "RGPD5" "PPP2R5C" "STK17B" "PPIL4"
## [19] "BTG1" "SSH2" "EPHA1" "PIP4K2A" "CXCR5" "PPP1R10"
## [25] "MALAT1"
## [1] 32
## [1] "GLT8D1" "FAR2" "SH3BP2" "KIF4A" "MAN2B1" "IFNG"
## [7] "SCPEP1" "DNPEP" "COQ3" "TPGS2" "SPPL2A" "LPP"
## [13] "TIFA" "MX1" "CCDC51" "SLC39A13" "PRF1" "CADM1"
## [19] "GM2A" "HIST1H4J" "HLA-DRA" "NCR3" "DNASE1" "ATP5J2"
## [25] "LMO7"
## [1] 33
## [1] "ERCC2" "GTF2H3" "NPL" "DRAM2" "NTAN1"
## [6] "C19orf55" "ZNF613" "ZNF765" "RUFY2" "POTEKP"
## [11] "TRGV10" "TRGV5" "TRAV8-2" "TRAV24" "TRGC2"
## [16] "TSEN15P1" "TRGV2" "CTC-338M12.4" "RP11-693N9.2" "ZEB1-AS1"
## [21] "LINC00426" "RP4-728D4.2" "PVT1" "TRGV7" "SCML1"
## [26] "RP13-488H8.1" "SLC7A5P1"
## [1] 34
## [1] "IMP4" "RPS17" "RPL34" "RPS12" "RPS25" "RPL21" "RPL5" "RPS10"
## [9] "RPS2" "RPL13A" "RPS27A" "RPL32" "RPS3A" "RPL7" "RPS3" "RPL30"
## [17] "RPL9" "RPS14" "RPL27A" "RPLP2" "RPS27" "RPS23" "RPS26" "RPL23A"
## [25] "RPS18"
## [1] 35
## [1] "OAS1" "MFSD9" "IFI27" "EFCAB4A"
## [5] "LCORL" "ZNF28" "CPT1B" "METTL6"
## [9] "TRDV1" "TRDC" "NAP1L1P3" "RP11-12M9.4"
## [13] "PSMA6P1" "LYPLA1P3" "CCT8P1" "HNRNPA1P21"
## [17] "RP11-288E14.2" "RBBP4P1" "GMPSP1" "RP11-613F22.5"
## [21] "RBBP4P5" "RP11-416A17.6" "TRAV30" "RP11-265N6.3"
## [25] "ATP5A1P3" "ACTBP9" "RP11-1094M14.7"
## [1] 36
## [1] "UBXN8" "SLC12A4" "YIPF2" "SLC41A2" "LINS" "MFSD6" "TMEM237"
## [8] "ALG8" "C2orf44" "GLB1" "LGALS9C" "SLC38A9" "YIPF6" "DBNDD2"
## [15] "PIK3IP1" "SLC38A1" "UAP1" "YPEL5" "NBPF14" "SLC38A2" "EPB41"
## [22] "NBPF10" "RGPD6" "CD55" "FAM169A" "NBPF16"
## [1] 37
## [1] "ICA1" "MED24" "NSMAF" "ZNRD1" "REC8" "POLR2I"
## [7] "LIG1" "POLE4" "EPAS1" "AKR1A1" "UXT" "CHTF18"
## [13] "SLC2A8" "TBCD" "PPP4R1" "MED11" "POLR2H" "IL15"
## [19] "MZT2A" "POLE" "PPARA" "CHAMP1" "STK19" "C17orf89"
## [25] "MRPL33"
## [1] 38
## [1] "RABGAP1" "CD84" "RGS1" "HAVCR1"
## [5] "EGR2" "TEP1" "TMEM19" "FAM50B"
## [9] "NAALADL1" "THAP2" "SH2D1B" "SGMS1"
## [13] "TRAV21" "MAPKAPK5-AS1" "RP11-271C24.3" "WDR65"
## [17] "CTB-4E7.1" "CTD-2521M24.9" "RP11-705C15.5" "ABLIM1"
## [21] "RIMKLB" "PHLDB3" "LDOC1" "KLRK1"
## [25] "HCG4P5" "ATP1B3-AS1"
## [1] 39
## [1] "NDUFAF7" "ACADVL" "NFE2L1" "MTIF2" "MRPS33" "NDUFAF5"
## [7] "CDK5RAP1" "EARS2" "MTFMT" "THG1L" "ATPAF1" "C6orf203"
## [13] "MTO1" "MRRF" "CETN3" "MALSU1" "MRPL55" "NDUFS4"
## [19] "C7orf55" "MRPL48" "ZNF782" "OXLD1" "CCDC109B" "TSHZ2"
## [1] 40
## [1] "MBNL3" "DDX49" "PDZD2" "RPSAP47"
## [5] "RP1-102E24.1" "UBA52P6" "RP1-182O16.1" "RPL19P12"
## [9] "RP11-350G8.3" "RPSAP4" "MGAT4A" "HECA"
## [13] "C1orf63" "PLXDC1" "TRABD2A" "RPS3AP26"
## [17] "AC021593.1" "LTB" "RPL10P3" "RPL9P8"
## [21] "RPL3P4" "RPL9P9" "RPL9P7" "RP11-285F7.2"
## [25] "MTND4P12" "ZNF10" "RP11-335G20.7"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_2"
## [1] "IL4R" "UTP6" "ACVR1" "SMUG1" "GLUL"
## [6] "GNG4" "ZNF816" "RPS27AP2" "CTB-33G10.1" "TXK"
## [11] "ARRDC2" "RASGRF2" "EGR1" "ACVR2A" "FOSB"
## [16] "JUND" "SKIL" "SORL1" "SGSM2" "GNAQ"
## [21] "LDLRAP1" "DHRS3" "TC2N" "TMEM150A" "DNHD1"
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 3547 response to bmp 5.727704e-06 0.9999999
## numDEInCat numInCat FDR
## 3547 5 11 0.02340913
##
## [1] "set_4"
## [1] "ID3" "PARP2" "MMS22L" "PLIN2"
## [5] "ATF3" "HIST1H2BC" "PLA2G6" "HIST2H2AA4"
## [9] "HIST1H2BN" "HIST1H3G" "RP11-386G11.10" "IFRD1"
## [13] "RGCC" "NR4A3" "RASGEF1B" "NR4A2"
## [17] "TIPARP" "PRMT10" "PFKFB3" "RBKS"
## [21] "CHD2" "ANKRD37" "MTND1P23" "PSMD6-AS2"
## [25] "KCNQ1OT1" "RP11-434H6.7"
## $reactome
## category
## 786 runx1 regulates genes involved in megakaryocyte differentiation and platelet function
## 10 activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 63 assembly of the orc complex at the origin of replication
## 122 chromatin modifications during the maternal to zygotic transition mzt
## 209 dna methylation
## 249 ercc6 csb and ehmt2 g9a positively regulate rrna expression
## 746 rho gtpases activate pkns
## 879 sirt1 negatively regulates rrna expression
## 639 prc2 methylates histones and dna
## 285 formation of the beta catenin tcf transactivating complex
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 786 4.313170e-06 0.9999999 5 13
## 10 2.519897e-05 0.9999996 4 9
## 63 2.519897e-05 0.9999996 4 9
## 122 2.519897e-05 0.9999996 4 9
## 209 2.519897e-05 0.9999996 4 9
## 249 2.519897e-05 0.9999996 4 9
## 746 2.519897e-05 0.9999996 4 9
## 879 2.519897e-05 0.9999996 4 9
## 639 4.141248e-05 0.9999991 4 10
## 285 6.416829e-05 0.9999984 4 11
## FDR
## 786 0.003219168
## 10 0.003219168
## 63 0.003219168
## 122 0.003219168
## 209 0.003219168
## 249 0.003219168
## 746 0.003219168
## 879 0.003219168
## 639 0.004702617
## 285 0.005961818
##
## $immune
## category over_represented_pvalue
## 1235 gse17974 0h vs 0.5h in vitro act cd4 tcell dn 2.969641e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 1235 1 6 15 0.00151422
##
## [1] "set_8"
## [1] "TRPT1" "TRBV4-2" "TRAV12-2" "RP11-383G10.3"
## [5] "RPS19P1" "NPM1P19" "Z97634.3" "RP11-32B5.1"
## [9] "NDUFA9P1" "RP11-33B1.1" "HNRNPA1P50" "DGKA"
## [13] "TCF7" "CCR7" "PCNXL2" "CDC42EP3"
## [17] "ZBTB20" "DENND5A" "POU6F1" "SELL"
## [21] "RPS26P6" "RP11-91K8.4" "WHAMMP2" "TMEM9B-AS1"
## [25] "RP11-747H7.3" "CTD-2017D11.1" "RP11-51J9.5"
## $immune
## category
## 56 goldrath eff vs memory cd8 tcell dn
## 3792 gse40274 ctrl vs eos transduced activated cd4 tcell dn
## 4851 gse9650 naive vs eff cd8 tcell up
## 4974 kaech naive vs day8 eff cd8 tcell up
## 2082 gse23568 ctrl vs id3 transduced cd8 tcell up
## 4086 gse43863 day6 eff vs day150 mem ly6c int cxcr5pos cd4 tcell dn
## 4844 gse9650 effector vs memory cd8 tcell dn
## 4969 kaech day8 eff vs memory cd8 tcell dn
## 2079 gse23568 ctrl transduced vs wt cd8 tcell dn
## 2746 gse2935 uv inactivated vs live sendai virus inf macrophage up
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 56 5.535430e-06 0.9999999 5 23
## 3792 8.549934e-06 0.9999998 5 25
## 4851 1.261357e-05 0.9999996 5 27
## 4974 1.275095e-05 0.9999996 5 27
## 2082 2.443384e-05 0.9999995 4 15
## 4086 3.363985e-05 0.9999992 4 16
## 4844 4.275140e-05 0.9999982 5 34
## 4969 4.302329e-05 0.9999982 5 34
## 2079 5.471493e-05 0.9999985 4 18
## 2746 5.565429e-05 0.9999985 4 18
## FDR
## 56 0.01625427
## 3792 0.01625427
## 4851 0.01625427
## 4974 0.01625427
## 2082 0.02491763
## 4086 0.02742197
## 4844 0.02742197
## 4969 0.02742197
## 2079 0.02837812
## 2746 0.02837812
##
## [1] "set_10"
## [1] "SMG6" "DUSP12" "MICALL1" "CNOT2" "RCOR3" "MTFR1L"
## [7] "CCDC77" "METTL8" "FOPNL" "CASP1" "KSR1" "VPS37A"
## [13] "TMEM208" "TMEM126A" "CEP63" "CNOT10" "CEP57L1" "RN7SL749P"
## [19] "TNRC6C" "CLDND1" "TNRC6B" "CNOT6L" "BTG2" "RALGAPA1"
## [25] "PLA2G4B"
## $reactome
## category
## 981 transcriptional regulation by tp53
## 952 tp53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain
## 954 tp53 regulates transcription of cell cycle genes
## 172 deadenylation of mrna
## 171 deadenylation dependent mrna decay
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 981 2.090452e-06 0.9999999 7 35
## 952 2.226282e-06 1.0000000 4 6
## 954 1.011921e-05 0.9999999 4 8
## 172 3.489845e-05 0.9999998 3 4
## 171 1.709831e-04 0.9999977 3 6
## FDR
## 981 0.001137630
## 952 0.001137630
## 954 0.003447277
## 172 0.008916553
## 171 0.034948947
##
## $go_bp
## category
## 1917 nuclear transcribed mrna poly a tail shortening
## 1912 nuclear transcribed mrna catabolic process
## 1913 nuclear transcribed mrna catabolic process deadenylation dependent decay
## 3702 rna destabilization
## 1372 mrna catabolic process
## 2380 positive regulation of mrna metabolic process
## 3201 regulation of mrna catabolic process
## 3700 rna catabolic process
## 3202 regulation of mrna metabolic process
## 1456 negative regulation of amide metabolic process
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1917 2.977880e-09 1.0000000 6 8
## 1912 1.120755e-08 1.0000000 7 15
## 1913 2.182607e-08 1.0000000 6 10
## 3702 2.834440e-07 1.0000000 6 14
## 1372 5.185335e-07 1.0000000 7 24
## 2380 7.335956e-07 1.0000000 6 16
## 3201 1.124232e-06 1.0000000 6 17
## 3700 2.188583e-06 0.9999999 7 29
## 3202 4.655463e-06 0.9999998 6 21
## 1456 3.558517e-05 0.9999979 6 29
## FDR
## 1917 1.217060e-05
## 1912 2.290263e-05
## 1913 2.973439e-05
## 3702 2.896089e-04
## 1372 4.238493e-04
## 2380 4.997009e-04
## 3201 6.563908e-04
## 3700 1.118092e-03
## 3202 2.114097e-03
## 1456 1.454366e-02
##
## [1] "set_11"
## [1] "POLA2" "USP28" "WDR3" "WIPI1" "PIK3C3"
## [6] "ULK2" "WDR13" "IFIT3" "IFIT2" "L3HYPDH"
## [11] "RSAD2" "BCAS3" "PELP1" "BAP1" "WDR41"
## [16] "PHAX" "ATG13" "IFIT1" "PIK3R4" "MBD5"
## [21] "CATSPER2P1" "RAB12" "C9orf72" "FBXO32"
## $go_bp
## category over_represented_pvalue
## 2830 regulation of autophagy 1.512986e-06
## 154 autophagosome organization 2.206566e-06
## 4025 vacuole organization 6.714553e-06
## 1173 macroautophagy 8.685364e-06
## 2684 protein localization to phagophore assembly site 1.772104e-05
## 3639 response to starvation 6.471983e-05
## 1924 nucleophagy 6.891717e-05
## 3142 regulation of macroautophagy 8.208376e-05
## 1171 lysosomal transport 8.238985e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 2830 0.9999999 7 25 0.004509117
## 154 1.0000000 5 10 0.004509117
## 4025 0.9999998 5 12 0.008874270
## 1173 0.9999996 6 21 0.008874270
## 2684 1.0000000 3 3 0.014485176
## 3639 0.9999969 5 18 0.037414148
## 1924 0.9999996 3 4 0.037414148
## 3142 0.9999977 4 10 0.037414148
## 1171 0.9999977 4 10 0.037414148
##
## [1] "set_18"
## [1] "MAD1L1" "RNF10" "PTPN18" "GABPB1" "SMC4" "C3orf14"
## [7] "STK25" "CKS2" "CCNB1" "PMAIP1" "HIRIP3" "CCNB2"
## [13] "ANAPC10" "CTSB" "TBCA" "RRM2" "ASB8" "EDARADD"
## [19] "TDRD7" "HIST1H4C" "DDX3Y" "FAM117B" "NPAT" "PLK3"
## [25] "TSC22D2"
## $reactome
## category over_represented_pvalue
## 138 condensation of prometaphase chromosomes 1.472594e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 138 1 3 3 0.01504991
##
## [1] "set_21"
## [1] "TBPL1" "DUS4L" "LOXL3" "FANCL"
## [5] "CD160" "DHDDS" "NPC2" "MCEE"
## [9] "MT2A" "MTHFS" "GTF2A2" "USF1"
## [13] "KIAA1841" "NFU1" "MT1E" "MT1X"
## [17] "TECPR1" "TRAV13-1" "TSTD1" "RNU2-2P"
## [21] "UBE2D3P2" "PET100" "LINC00493" "RP11-1012A1.7"
## [25] "MIR142"
## $reactome
## category over_represented_pvalue
## 485 metallothioneins bind metals 9.853714e-06
## 737 response to metal ions 9.853714e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 485 1 3 3 0.005035248
## 737 1 3 3 0.005035248
##
## $go_bp
## category over_represented_pvalue
## 353 cellular response to cadmium ion 1.502551e-05
## 358 cellular response to copper ion 1.502551e-05
## 564 detoxification of copper ion 1.502551e-05
## 565 detoxification of inorganic compound 1.502551e-05
## 3548 response to cadmium ion 1.502551e-05
## 3555 response to copper ion 1.502551e-05
## 1055 intracellular zinc ion homeostasis 5.835770e-05
## 420 cellular response to zinc ion 5.864869e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 353 1.0000000 3 3 0.01023488
## 358 1.0000000 3 3 0.01023488
## 564 1.0000000 3 3 0.01023488
## 565 1.0000000 3 3 0.01023488
## 3548 1.0000000 3 3 0.01023488
## 3555 1.0000000 3 3 0.01023488
## 1055 0.9999997 3 4 0.02996215
## 420 0.9999997 3 4 0.02996215
##
## [1] "set_25"
## [1] "MFAP3" "TNFRSF9" "C14orf93" "SLC25A14" "SLC11A2"
## [6] "MDGA1" "CD86" "TNFSF10" "IFI6" "DPH6"
## [11] "IFI44L" "IFI44" "LAIR2" "TRANK1" "CXCR6"
## [16] "TRBV9" "TRAV19" "CRYGS" "AC104820.2" "MIR155HG"
## [21] "AC092580.4" "AKAP2" "CCL3L3" "RP11-345J4.6" "AMICA1"
## [26] "MUC20"
## $immune
## category over_represented_pvalue
## 4555 gse6269 healthy vs staph aureus inf pbmc up 4.004366e-06
## 2427 gse2706 2h vs 8h r848 stim dc dn 1.417185e-05
## 1337 gse18791 ctrl vs newcastle virus dc 6h dn 2.301492e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 4555 0.9999998 6 22 0.02041826
## 2427 0.9999995 5 16 0.03613114
## 1337 0.9999987 6 29 0.03911769
##
## [1] "set_27"
## [1] "REXO1" "ZNF683" "PDCL3P5" "AC098614.2"
## [5] "NPM1P33" "CALM2P3" "TCP1P1" "AC144530.1"
## [9] "CDC42P1" "RP3-395M20.8" "RP11-382J24.2" "HSPA8P5"
## [13] "AC006483.1" "AC139149.1" "MIR3661" "RASGRP2"
## [17] "CPQ" "FOXP1" "C1orf162" "PLAC8"
## [21] "FAM102A" "GPR183" "SATB1" "CTD-3092A11.1"
## [25] "RP11-632K20.7" "RP1-313I6.12"
## $immune
## category
## 595 gse14699 naive vs deletional tolerance cd8 tcell dn
## 1580 gse20727 h2o2 vs ros inhibitor treated dc up
## 3848 gse40274 lef1 vs foxp3 and lef1 transduced activated cd4 tcell dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 595 2.973401e-08 1.0000000 6 25
## 1580 1.997739e-05 0.9999996 4 19
## 3848 2.494993e-05 0.9999995 4 20
## FDR
## 595 0.0001516137
## 1580 0.0424065620
## 3848 0.0424065620
##
## [1] "set_30"
## [1] "EVI5" "CDKN3" "RAD51C" "STMN1"
## [5] "TXNDC17" "TROAP" "BORA" "GEMIN6"
## [9] "MITD1" "PAQR4" "CDCA7L" "C11orf82"
## [13] "ZFYVE19" "UBE2C" "TYMS" "LRTOMT"
## [17] "SESTD1" "TCTEX1D2" "NCKIPSD" "MDP1"
## [21] "RP11-378G13.2" "SAPCD1" "PAICSP4" "HMGB1P24"
## [25] "RP11-307P22.1" "RP11-265N6.2"
## $immune
## category
## 4962 howard nk cell inact monov influenza a indonesia 05 2005 h5n1 age 18 49yo 3dy up
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4962 7.935581e-07 1 5 10
## FDR
## 4962 0.004046353
##
## [1] "set_32"
## [1] "GLT8D1" "FAR2" "SH3BP2" "KIF4A" "MAN2B1" "IFNG"
## [7] "SCPEP1" "DNPEP" "COQ3" "TPGS2" "SPPL2A" "LPP"
## [13] "TIFA" "MX1" "CCDC51" "SLC39A13" "PRF1" "CADM1"
## [19] "GM2A" "HIST1H4J" "HLA-DRA" "NCR3" "DNASE1" "ATP5J2"
## [25] "LMO7"
## $go_bp
## category over_represented_pvalue
## 2895 regulation of cell killing 4.566378e-06
## 2172 positive regulation of cell killing 7.711744e-06
## 314 cell killing 2.617120e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 2895 0.9999998 6 22 0.01575895
## 2172 0.9999998 5 14 0.01575895
## 314 0.9999985 6 29 0.03565390
##
## $immune
## category over_represented_pvalue
## 3539 gse37605 treg vs tconv c57bl6 foxp3 fusion gfp dn 1.925098e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 3539 1 5 10 0.009816073
##
## [1] "set_33"
## [1] "ERCC2" "GTF2H3" "NPL" "DRAM2" "NTAN1"
## [6] "C19orf55" "ZNF613" "ZNF765" "RUFY2" "POTEKP"
## [11] "TRGV10" "TRGV5" "TRAV8-2" "TRAV24" "TRGC2"
## [16] "TSEN15P1" "TRGV2" "CTC-338M12.4" "RP11-693N9.2" "ZEB1-AS1"
## [21] "LINC00426" "RP4-728D4.2" "PVT1" "TRGV7" "SCML1"
## [26] "RP13-488H8.1" "SLC7A5P1"
## $reactome
## category over_represented_pvalue
## 283 formation of rna pol ii elongation complex 0.0001637134
## 286 formation of the early elongation complex 0.0001637134
## 370 hiv transcription elongation 0.0001637134
## 506 mrna capping 0.0001637134
## 766 rna polymerase i transcription initiation 0.0001681170
## 767 rna polymerase i transcription termination 0.0001681170
## 371 hiv transcription initiation 0.0003302842
## 768 rna polymerase ii pre transcription events 0.0003302842
## 970 transcription of the hiv genome 0.0003302842
## 281 formation of incision complex in gg ner 0.0003557590
## under_represented_pvalue numDEInCat numInCat FDR
## 283 0.9999997 2 5 0.02863592
## 286 0.9999997 2 5 0.02863592
## 370 0.9999997 2 5 0.02863592
## 506 0.9999997 2 5 0.02863592
## 766 0.9999997 2 5 0.02863592
## 767 0.9999997 2 5 0.02863592
## 371 0.9999991 2 7 0.03635857
## 768 0.9999991 2 7 0.03635857
## 970 0.9999991 2 7 0.03635857
## 281 0.9999990 2 7 0.03635857
##
## [1] "set_34"
## [1] "IMP4" "RPS17" "RPL34" "RPS12" "RPS25" "RPL21" "RPL5" "RPS10"
## [9] "RPS2" "RPL13A" "RPS27A" "RPL32" "RPS3A" "RPL7" "RPS3" "RPL30"
## [17] "RPL9" "RPS14" "RPL27A" "RPLP2" "RPS27" "RPS23" "RPS26" "RPL23A"
## [25] "RPS18"
## $reactome
## category
## 21 activation of the mrna upon binding of the cap binding complex and eifs and subsequent binding to 43s
## 117 cellular response to starvation
## 255 eukaryotic translation elongation
## 256 eukaryotic translation initiation
## 387 influenza infection
## 471 metabolism of amino acids and derivatives
## 547 nonsense mediated decay nmd
## 691 regulation of expression of slits and robos
## 734 response of eif2ak4 gcn2 to amino acid deficiency
## 783 rrna processing
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat FDR
## 21 0 1 13 15 0
## 117 0 1 24 33 0
## 255 0 1 24 31 0
## 256 0 1 24 30 0
## 387 0 1 24 37 0
## 471 0 1 24 42 0
## 547 0 1 24 31 0
## 691 0 1 24 31 0
## 734 0 1 24 30 0
## 783 0 1 25 40 0
##
## $go_bp
## category over_represented_pvalue
## 515 cytoplasmic translation 0.000000e+00
## 3693 ribosome biogenesis 1.928974e-09
## 3691 ribosomal small subunit biogenesis 7.669988e-09
## 3718 rrna metabolic process 1.025484e-05
## 3692 ribosome assembly 2.168596e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 515 1.0000000 24 33 0.000000e+00
## 3693 1.0000000 11 35 3.941858e-06
## 3691 1.0000000 8 16 1.044908e-05
## 3718 0.9999994 7 26 1.047789e-02
## 3692 0.9999997 4 6 1.772611e-02
##
## $immune
## category
## 54 gaucher pbmc yf vax stamaril unknown age 7dy dn
## 463 gse14000 translated rna vs mrna dc dn
## 1628 gse2124 ctrl vs lymphotoxin beta treated mln up
## 1944 gse22886 naive bcell vs neutrophil up
## 1974 gse22886 naive tcell vs dc up
## 2104 gse2405 0h vs 24h a phagocytophilum stim neutrophil up
## 2109 gse2405 0h vs 9h a phagocytophilum stim neutrophil dn
## 3108 gse34205 healthy vs flu inf infant pbmc up
## 4014 gse41978 id2 ko vs id2 ko and bim ko klrg1 low effector cd8 tcell dn
## 4016 gse41978 klrg1 high vs low effector cd8 tcell dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat FDR
## 54 0 1 14 32 0
## 463 0 1 12 26 0
## 1628 0 1 10 19 0
## 1944 0 1 11 25 0
## 1974 0 1 14 33 0
## 2104 0 1 19 40 0
## 2109 0 1 19 37 0
## 3108 0 1 12 25 0
## 4014 0 1 12 32 0
## 4016 0 1 14 30 0
##
## [1] "set_36"
## [1] "UBXN8" "SLC12A4" "YIPF2" "SLC41A2" "LINS" "MFSD6" "TMEM237"
## [8] "ALG8" "C2orf44" "GLB1" "LGALS9C" "SLC38A9" "YIPF6" "DBNDD2"
## [15] "PIK3IP1" "SLC38A1" "UAP1" "YPEL5" "NBPF14" "SLC38A2" "EPB41"
## [22] "NBPF10" "RGPD6" "CD55" "FAM169A" "NBPF16"
## $reactome
## category
## 880 slc mediated transmembrane transport
## 997 transport of inorganic cations anions and amino acids oligopeptides
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 880 1.686105e-05 0.9999997 4 9
## 997 7.902577e-05 0.9999993 3 5
## FDR
## 880 0.01723200
## 997 0.04038217
##
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 864 glutamine transport 1.0726e-05 1
## numDEInCat numInCat FDR
## 864 3 3 0.04383717
##
## [1] "set_39"
## [1] "NDUFAF7" "ACADVL" "NFE2L1" "MTIF2" "MRPS33" "NDUFAF5"
## [7] "CDK5RAP1" "EARS2" "MTFMT" "THG1L" "ATPAF1" "C6orf203"
## [13] "MTO1" "MRRF" "CETN3" "MALSU1" "MRPL55" "NDUFS4"
## [19] "C7orf55" "MRPL48" "ZNF782" "OXLD1" "CCDC109B" "TSHZ2"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 495 mitochondrial translation 5.271263e-09 1.0000000
## 986 translation 3.177704e-05 0.9999979
## numDEInCat numInCat FDR
## 495 6 9 5.387230e-06
## 986 7 46 1.623806e-02
##
## $go_bp
## category over_represented_pvalue
## 1301 mitochondrial gene expression 0.000000e+00
## 1311 mitochondrial translation 3.526225e-09
## 1307 mitochondrial rna metabolic process 9.799058e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 1301 1.0000000 9 16 0.000000e+00
## 1311 1.0000000 7 13 7.205842e-06
## 1307 0.9999999 4 7 1.334958e-02
##
## $immune
## category
## 4823 gse9316 cd4 tcell balbc vs th17 enri cd4 tcell skg pma iono stim fr4neg up
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4823 9.056117e-06 0.9999997 5 14
## FDR
## 4823 0.04617714Session information
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8958692 478.5 17165476 916.8 NA 17165476 916.8
## Vcells 19171056 146.3 57891911 441.7 65536 78485130 598.8## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0
## [2] GenomicFeatures_1.50.4
## [3] GenomicRanges_1.50.2
## [4] GenomeInfoDb_1.34.9
## [5] org.Hs.eg.db_3.16.0
## [6] AnnotationDbi_1.60.2
## [7] IRanges_2.32.0
## [8] S4Vectors_0.36.2
## [9] Biobase_2.58.0
## [10] BiocGenerics_0.44.0
## [11] goseq_1.50.0
## [12] geneLenDataBase_1.34.0
## [13] BiasedUrn_2.0.10
## [14] fgsea_1.24.0
## [15] biomaRt_2.54.1
## [16] limma_3.54.2
## [17] tidyr_1.3.0
## [18] ggpubr_0.6.0
## [19] ggplot2_3.4.2
## [20] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 tools_4.2.3
## [9] backports_1.4.1 bslib_0.4.2
## [11] utf8_1.2.3 R6_2.5.1
## [13] mgcv_1.8-42 DBI_1.1.3
## [15] colorspace_2.1-0 withr_2.5.0
## [17] tidyselect_1.2.0 prettyunits_1.1.1
## [19] bit_4.0.5 curl_5.0.1
## [21] compiler_4.2.3 cli_3.6.1
## [23] xml2_1.3.4 DelayedArray_0.24.0
## [25] rtracklayer_1.58.0 sass_0.4.5
## [27] scales_1.2.1 rappdirs_0.3.3
## [29] Rsamtools_2.14.0 stringr_1.5.0
## [31] digest_0.6.31 rmarkdown_2.21
## [33] XVector_0.38.0 pkgconfig_2.0.3
## [35] htmltools_0.5.5 MatrixGenerics_1.10.0
## [37] dbplyr_2.3.2 fastmap_1.1.1
## [39] rlang_1.1.0 rstudioapi_0.14
## [41] RSQLite_2.3.1 BiocIO_1.8.0
## [43] jquerylib_0.1.4 generics_0.1.3
## [45] jsonlite_1.8.4 BiocParallel_1.32.6
## [47] dplyr_1.1.2 car_3.1-2
## [49] RCurl_1.98-1.12 magrittr_2.0.3
## [51] GO.db_3.16.0 GenomeInfoDbData_1.2.9
## [53] Matrix_1.6-4 Rcpp_1.0.10
## [55] munsell_0.5.0 fansi_1.0.4
## [57] abind_1.4-5 lifecycle_1.0.3
## [59] stringi_1.7.12 yaml_2.3.7
## [61] carData_3.0-5 SummarizedExperiment_1.28.0
## [63] zlibbioc_1.44.0 BiocFileCache_2.6.1
## [65] grid_4.2.3 blob_1.2.4
## [67] parallel_4.2.3 crayon_1.5.2
## [69] lattice_0.20-45 splines_4.2.3
## [71] Biostrings_2.66.0 cowplot_1.1.1
## [73] hms_1.1.3 KEGGREST_1.38.0
## [75] knitr_1.44 pillar_1.9.0
## [77] rjson_0.2.21 ggsignif_0.6.4
## [79] codetools_0.2-19 fastmatch_1.1-3
## [81] XML_3.99-0.14 glue_1.6.2
## [83] evaluate_0.20 png_0.1-8
## [85] vctrs_0.6.2 gtable_0.3.3
## [87] purrr_1.0.1 cachem_1.0.7
## [89] xfun_0.39 broom_1.0.4
## [91] restfulr_0.0.15 rstatix_0.7.2
## [93] tibble_3.2.1 GenomicAlignments_1.34.1
## [95] memoise_2.0.1